Nechooshtan, G. | bioRxiv Science

bioRxiv2026

3'UTR-directed control of poly(A) tail dynamics and mRNA stability in vertebrate embryos

Post-transcriptional regulation determines mRNA fate through multiple interconnected layers of control, and is particularly important in early embryos. However, how 3'UTR sequences coordinate these different regulatory layers remains poorly characterized. Here, we develop multi-UTR, a massively parallel reporter assay that simultaneously tracks poly(A) tail lengths, 3' terminal nucleotide additions, and mRNA stabilities for thousands of 3'UTR sequences across early zebrafish embryogenesis. We show that embryos use a combination of global and 3'UTR-encoded regulatory programs to progressively remodel mRNA tails. Using reporters with various initial tail lengths, we find that the embryonic cytoplasm rapidly overrides pre-set poly(A) lengths. As development proceeds, 3'UTRs drive tail length diversity and longer tails become progressively associated with increased stability. Strikingly, this association is affected by productive translation: in non-coding reporters, the tail length-stability relationship inverts, such that shorter poly(A) tails are associated with greater stability. Poly(A) tail remodeling is accompanied by two waves of terminal nucleotide additions, early guanylation and later uridylation, that mark distinct regulatory states. Together, our results uncover how the 3'UTR regulatory code operates across multiple layers of regulation to dynamically shape maternal mRNA fate during embryogenesis, and establish multi-UTR as a general platform for decoding post-transcriptional regulatory programs.

molecular biology↗

bioRxiv2023

Single-cell temporal dynamics reveals the relative contributions of transcription and degradation to cell-type specific gene expression in zebrafish embryos

AbstractDuring embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the underlying regulation of mRNA transcription and degradation remains a challenge, especially within whole embryos with diverse cellular identities. Here, we collect temporal cellular transcriptomes of zebrafish embryos, and decompose them into their newly-transcribed (zygotic) and pre-existing (maternal) mRNA components by combining single-cell RNA-Seq and metabolic labeling. We introduce kinetic models capable of quantifying regulatory rates of mRNA transcription and degradation within individual cell types during their specification. These reveal different regulatory rates between thousands of genes, and sometimes between cell types, that shape spatio-temporal expression patterns. Transcription drives most cell-type restricted gene expression. However, selective retention of maternal transcripts helps to define the gene expression profiles of germ cells and enveloping layer cells, two of the earliest specified cell-types. Coordination between transcription and degradation restricts expression of maternal-zygotic genes to specific cell types or times, and allows the emergence of spatio-temporal patterns when overall mRNA levels are held relatively constant. Sequence-based analysis links differences in degradation to specific sequence motifs. Our study reveals mRNA transcription and degradation events that control embryonic gene expression, and provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response.

genomics↗